When a login here (GMT +1) happens just after midnight, the displayed date is the date before.

The plugin saves time() in the user meta, and in WordPress this means GMT. When displayed the timestamp is regarded local. Suggest this change:

$value = get_date_from_gmt( date( 'Y-m-d H:i:s', $last_login ), get_option( 'date_format' ) );

in the manage_users_custom_column filter.